SLAC and SSRL visit!

This morning Sarah took Mariela, Mariela's mentor, and me to the SLAC campus to see the SSRL: the Stanford Synchrotron Radiation Lightsource. It was so neat to see! Here's some pictures:

My temporary nametag

This curved structure is the small circle where electrons are first accelerated.

Once the electrons are moving fast enough, they enter this larger curved structure. In here, they release X-rays each time they change direction.

The X-rays are captured in channels tangential to the main structure and eventually arrive in machines such as this one, which use the X-rays for various purposes.

An example of a sample whose surface will be scanned using X-rays to determine the placement of different elements within the samples

ICP-MS

Today we ran our samples on the ICP-MS machine!
We took our samples off of the shakers first thing in the morning.  From there, we had to make our standard solutions and controls, measure our samples into ICP-MS tubes, acidify our samples, and put them in the correct order to be measured by the ICP-MS machine.

The general procedure with standard solutions is to first make a high standard, which contains each of the components to be measured at concentrations higher than the expected maximum concentration in any sample. The concentrations of each component in this high standard must be known very exactly, so prepared and certified standardized solutions are used. The high standard is then diluted a few times so that exact concentrations can be known and the ICP-MS machine can calibrate itself. For this, we needed to run around the labs trying to find the correct stock standards for all of the elements we were measuring (quite a few). We found all of them except barium, so we'll need to find a barium standard and run the samples again on the ICP-OES machine later.

Each ICP-MS tube requires about 6 mL of solution, so we had to label the tubes and measure in solution (the ICP-MS machine needs about 4.5 mL of solution to collect three data points for a particular sample). After filling all the tubes, I added a small amount of concentrated nitric acid to each tube in order to bring the solution to the optimal pH. I capped all the tubes, inverted them a few times to mix them, and then we had to make a spreadsheet indicating the measurement order of the tubes. After each group of samples, the machine needs to run a blank (in this case, just dilute nitric acid), and roughly every 10 samples a QC (quality control) sample is run made from the standard solution. That way, if the measurements are off, the machine can re-calibrate itself frequently. But because of this, it's super important that the standard solution's concentration be known extremely well!

Finally, we put our tubes in order and placed the rack of samples into the machine. The ICP-MS machine has a little robotic suction arm that dips into the samples one by one and sucks up some of the liquid. Everything is automated, and it was fun to watch. We'll get to see our data tomorrow and hopefully it'll be of good quality.

Phyllosilicates galore

Today was a good example of the varied rhythm of research. Whereas yesterday was mostly packed with lab work, today I was based in the office, reading materials on different types of clay molecules in order to better understand the work we're doing in the lab. Our reading materials were from lecture supplements to Scott's soils course (Scott as in Scott Fendorf, the faculty member who runs our project and many others). I learned all about tetrahedral and octahedral oxygen-based clay structures... which sounded scary until Sarah brought out some models!

A simple model of a phyllosilicate comprised mainly of oxygen atoms (red).

A model of the muscovite we work with. One can see clearly on this image that there are two main "layers" connected by a sheet of potassium atoms (yellow, center). This space between the layers allows the phyllosilicate to physically expand in the presence of certain substances such as water or some ions.

The important thing to understand for our work from these structures is that these clays have a permanent negative charge. Many of the non-oxygen ions originally present in the structure are exchanged through long-term processes for ions with a lower charge, giving the once-neutral clays a negative charge. This greatly affects their behavior and has implications for our research on different ions' interactions with clay in water.

We also had the first of our weekly SESUR/SURGE/MUIR lunch seminars (between the three undergraduate research programs in the School of Earth Sciences). Today Assistant Professor Nicole Ardoin came to talk to us about her work studying environmental learning behaviors. It was a good way to take a break from the lab and meet the other students doing similar work on campus this summer.

Expect the unexpected

My second day of SESUR research was a full plunge into lab work. The most important lesson I learned today was to always expect the unexpected during the research process. I went to bed last night excited to measure the difference in arsenic sorption between standard and field-sample clays in the presence of calcium ions... and arrived in the lab this morning to learn that we'd be tweaking the experiment significantly in order to focus on the effects of different types of cations on arsenic sorption on standard clays. If that was confusing, basically where I thought I would be comparing two clay types I'll now only be using one, and where I thought I'd only be dealing with one type of cation I'll now be working on an experiment with three - calcium, barium, and lithium.

It was an immediate lesson in flexibility - something Richard Nevle, the fantastic SESUR program director, had reminded us many times is essential to all types of research. Having my "mini-project" completely change course on day two certainly reinforced that point for me in a more concrete way. In the spirit of adapting, I didn't hesitate, and Sarah and I jumped right into work. We were accompanied by Mariela, a SURGE (Summer Undergraduate Research in Geoscience & Engineering, a similar program to SESUR but open to students from other universities and aimed at juniors and seniors) participant whose primary mentor is also currently traveling, like mine.

Today was a long day so that we could finish preparing our samples and give them time to shake for about 40 hours before our scheduled time on the ICP-MS (Inductively Coupled Plasma Mass Spectroscopy, and yes, I've learned to say the full name correctly!) machine on Thursday afternoon. We had to label 38 tiny bottles (and some larger ones), make 19 carefully-mixed stock solutions with different cation concentrations, pipette them into the little bottles, and (the most mind-numbingly boring part of all) measure 30 mg of clay powder into each bottle. I had no idea how small 30 mg of powder is until I spent an hour getting each sample to exactly 30 mg on the balance, adding or removing a few particles of clay powder at a time. I certainly didn't expect to do that either, but it had to be done. I wonder what unexpected things will happen for the rest of the summer...

First day!

Today was my first day as an undergraduate researcher at Stanford's School of Earth Sciences Undergraduate Research program (SESUR). It was an interesting but quick first day!

My postdoc research advisor Sam is currently in China collecting samples, some of which I'll be using for my project. But since she's gone, but the SESUR program has already begun, I'm starting work under the supervision of her lab-mate Sarah. While Sam studies coal pollution on agricultural lands in China, Sarah studies groundwater arsenic contamination in Orange County. Working with Sarah, however, will give me a chance to familiarize myself with how the lab works, get to understand certain aspects of soil geochemistry, and "practice" doing lab work and data analysis on a short two-week "mini-project" so that by the time Sam comes back with the samples, I'll be ready to go.

This morning I was up bright and early, since I was excited to start - but an email from Sarah had told me she'd be busy with meetings until 1 p.m. So I went for a jog to clear my head and then spent the morning studying some materials she had sent me, including some papers and her own poster from a recent conference. I tripped over phrases like "phyllosilicate clays" and "sorption isotherms", but quick googling helped to clear up most of what I didn't understand.

After lunch, I headed over to the Green Earth Sciences building, where the Fendorf lab (Sarah and Sam's lab) is located. Sarah and I first went over her project's progress so far, and she cleared up my remaining questions, and then we decided on a mini-project that I would be able to undertake over the course of the next couple weeks. I'll be using a batch reactor technique to measure arsenic sorption onto charged clay surfaces in the presence of different concentrations of calcium ions. I'm excited!

We spent the rest of the day in the lab and on Excel figuring out the different quantities of solutions we would need and checking that we had enough bottles and stock solution. I also received a brand-new lab notebook that I'll get to use for the summer. Tomorrow I'll meet some more summer interns, and we have some safety tours and things we need to do before we're really allowed to work in the lab. Can't wait to begin!